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A red ribbon hangs from the pillars of a courthouse in Washington to commemorate World AIDS Day.
Reuters/Jim Young
The history of HIV in America is being rewritten by genetic sequencing technology
GONE VIRAL

Scientists definitively debunked the Patient Zero myth using advanced viral genome tracking

By Katherine Ellen Foley

“I’ve got gay cancer. I’m gonna die, and so are you.”

Gaëtan Dugas, a flight attendant in the 1980s, would reportedly say those now-infamous words to men after he had unprotected sex with them, according to Randy Shilts, a journalist at the San Francisco Chronicle and author of the 1987 book And the Band Played On. Shilts named Dugas the “Patient Zero” of the human immunodeficiency virus (HIV) epidemic in the US, essentially blaming him for bringing the disease to America.

Undoubtedly, Dugas passed on HIV to hundreds or even thousands of men he slept with, according to Shilts, which is why it was possible to trace at least part of the first documented (pdf) outbreak in Los Angeles in 1981 back to him. But since the release of Shilt’s book, scientists have been able to wield new genetic technologies to more clearly identify the path HIV has razed through human populations.

Today (Oct. 26), scientists from the University of Arizona and the University of Cambridge published (paywall) work in Nature that uses the most precise viral genome tracking methods available to show that HIV was present in America as early as 1970 or 1971 in New York, about 10 years before it was found Los Angeles. Additionally, they fully mapped out the genetic code of the specific instance of the virus Dugas carried and definitively proved he was not the first to bring it to the US.

HIV is a virus that allows another pathogen to do the dirty work of killing its host. It lurks in the body without causing any symptoms, until all of a sudden it starts replicating its genetic material inside immune cells found in the blood, genital secretions, and breast milk. In doing so, the virus destroys these cells, and the body’s immune system weakened and is eventually rendered defenseless against infections normally fought off relatively easily—the condition called acquired immunodeficiency syndrome, or AIDS.

HIV is a virus that allows another pathogen to do the dirty work of killing its host.

One of the reasons that we don’t have a vaccine for HIV is because of how often the virus makes mistakes during the replicating process. “The virus goes through a round of replications in infected individuals every two or three days, and has a very sloppy set of enzymes that introduce mutations quite often,” says Michael Worobey, an evolutionary biologist at the University of Arizona and lead author of the recent paper.

HIV only has a single strand of genetic code called RNA. DNA has two sets of code twisted together; with the help of an enzyme, each side acts like a spell check for the other during the copying process. But RNA lacks this spell check, and the genetic code for HIV often has minor typos—not enough for it to cease being a functioning virus, but enough to make it genetically distinct from previous generations.

Although scientists can’t tell which mutations are likely to occur next—and thus can’t design an effective vaccine—they know how frequently they happen, which helps them understand how long the virus has been in a given population. When HIV shows up in a new place, “from that point, on you can kind of look at it like planting a seed.” Worobey says. Each mutation is like a new branch that grows off the original virus; for example, in Kinshasa, Democratic Republic of Congo, where HIV has been for a long time, the virus has enough branches to look like an old oak tree.

“From that point, on you can kind of look at it like planting a seed.”

Tracking the rate of mutations in the virus enabled scientists to follow the virus back to Cameroon in the early 1900s. The HIV that we see today was originally a mutation of the simian immunodeficiency virus (SIV), which occurs in about 40 different species of monkeys, including chimpanzees. In 2006, scientists published (paywall) work isolating the specific group of chimps in Cameroon that carried the virus that made the jump to humans.

How exactly that happens is not known. “The best hypothesis is the cut hunter hypothesis,” David Quammen, a journalist who’s written extensively about HIV, told Radiolab in 2011. Likely, a hunter was killing an SIV-positive chimp as bushmeat, and at some point cut himself, mixing the animal’s blood with his. That strain of SIV had evolved just enough to be able to survive and thrive in a human environment.

“The virus needs to have the stars aligned correctly” for it to spread from chimps to humans, and then onto so many people, Worobey says. In the US, an estimated 1.2 million people—mostly men who have sex with men—are living with HIV; globally, that number is closer to 37 million.

Worobey and his team analyzed blood samples taken 40 years ago to try to get a better understanding of how HIV has mutated over time as it moved through the US. RNA is a delicate molecule, and old samples of HIV-infected blood tend to become damaged by thawing and refreezing. But the researchers needed to make copies of all the genetic material in a given virus to get a clear picture of its mutations. So, they developed a technique called “RNA jackhammering.”

Rather than trying to make many copies of the entire length of viral genetic material at once, they isolated several shorter bits of RNA they wanted to copy. They made sure each clip overlapped slightly with other genetic material. When they made copies of these shorter chains, the overlapping regions acted as a guide for them to complete the whole genome. “In eight of these old samples, it worked well enough to find complete genomes,” Worobey says.

The group calculated the number of mutations in the samples, which were from the mid-1970s, and determined that HIV had been in America as early as 1970 or 1971. “What you see is that by the late 1970s, [the strains of HIV from] New York City [are] already a pretty mature sapling that’s eight feet high and has a whole bunch of branches the thickness of your wrist,” he says. “Whereas in San Francisco at the same point in time, you go and look there and it’s a tiny little seedling.”

The team then sequenced the genome of the version of HIV that had infected Dugas—and found it had mutations drastically different from earlier cases of American HIV.

Now, with biological evidence from Dugas’ HIV itself, they can definitively end that misnomer.

Richard McKay, a public health historian at the University of Cambridge and co-author of the paper, has argued—along with many others—that Dugas wasn’t entirely responsible for bring HIV to the US. The misunderstanding, the researchers write in the paper published today, was due to a misinterpreted reference.

Originally when California researchers were investigating HIV, they referred to Dugas as “Patient O,” for “Outside of California”—Dugas was from Quebec City, Canada. “As investigators numbered the cluster cases by date of symptom onset, the letter ‘O’ was misinterpreted as the number ‘0,’ and the non-Californian AIDS patient entered the literature with that title,” the authors write. Now, with biological evidence from Dugas’ HIV itself, they can definitively end that misnomer.

Worobey says he hopes to employ the same viral genome tracking methods the team used to rewrite the history books to develop prevention methods for the future. “The same techniques we use to look backwards are ones that are going to play a crucial role in moving forward to a place where we get close to eliminating the virus,” says Worobey.

The key is understanding where HIV will go in the future. “We now know that this virus didn’t just come out of nowhere in Los Angeles in 1981,” he says. As they model current outbreaks, they can try to predict which regions may need interventions—like better access to antiviral therapies and early detection methods—to slow the spread of the dangerous virus.